unload too

src/atom/extension-manager.coffee

@@ -6,6 +6,7 @@ class ExtensionManager
 
   constructor: ->
     atom.on 'window:load', @loadExtensions
+    atom.on 'window:close', @unloadExtensions
 
   loadExtensions: =>
     extension.shutdown() for name, extension of @extensions
@@ -28,3 +29,5 @@ class ExtensionManager
         console.warn "Extension #{extension::name} failed to startup."
         console.warn error
 
+  unloadExtensions: =>
+    extension.shutdown() for name, extension of @extensions

src/atom/window.coffee

@@ -34,8 +34,6 @@ windowAdditions =
     atom.trigger 'window:load'
 
   shutdown: ->
-    extension.shutdown() for name, extension of @extensions
-
     frame = $atomController.window.frame
     x = frame.origin.x
     y = frame.origin.y
@@ -51,8 +49,7 @@ windowAdditions =
     $atomController.window.title = title
 
   reload: ->
-    @shutdown()
-    $atomController.close
+    @close()
     OSX.NSApp.createController @path
 
   open: (path) ->